As a key tool to optimize the use of financial funds and the supply of public services, budget performance management plays an important role in public management. Based on the budget performance management reform practice of 66 districts and counties in Zhejiang Province from 2017 to 2023, this paper applies stochastic frontier modeling to assess the actual impact of the reform on public service output efficiency. Further, it explores the moderating effect in three dimensions: fiscal regulatory, government transparency, and Internet service capacity. The results show that: (1) The comprehensive budget performance management reform significantly improves the public service output efficiency. (2) Fiscal regulatory capacity, government transparency and Internet service capacity positively moderated the above reform effects, and have significant threshold effects. (3) In terms of economic consequences, after the implementation of the reform, the improvement of public service output efficiency in the field of education enhanced the level of regional innovation. This paper provides empirical evidence for an in-depth understanding of the reform’s effects, which provides important insights into the improvement of subsequent reforms and the deepening of China’s budget performance management system.